library(knitr)
packageVersion("knitr")
## [1] '1.20'
library(energy)
packageVersion("energy")
## [1] '1.7.5'
library(broom)
packageVersion("broom")
## [1] '0.5.0'
library(plyr)
packageVersion("plyr")
## [1] '1.8.4'
library(kableExtra)
packageVersion("kableExtra")
## [1] '0.9.0'
library(foreach)
packageVersion("foreach")
## [1] '1.4.4'
library(doParallel)
## Loading required package: iterators
## Loading required package: parallel
packageVersion("doParallel")
## [1] '1.0.14'
set.seed(0)
load(file = "p53_curated.Rdata")
epsilon=1e-6
nominal_dcor_pvalues <- sapply(1:pathway_number, function(x) (epsilon+(sum(surrogate_dcor[[x]]>dcor_results[x])))/(1+num_simulation))
names(nominal_dcor_pvalues) <- names( pathway_collapsed)
head(sort(nominal_dcor_pvalues),10)
## REACTOME_GAB1_SIGNALOSOME
## 0.0000000001
## REACTOME_PI_3K_CASCADE
## 0.0000000001
## REACTOME_PIP3_ACTIVATES_AKT_SIGNALING
## 0.0000000001
## GHANDHI_DIRECT_IRRADIATION_UP
## 0.0000000001
## QUINTENS_EMBRYONIC_BRAIN_RESPONSE_TO_IR
## 0.0000000001
## MACAEVA_PBMC_RESPONSE_TO_IR
## 0.0000000001
## KEGG_APOPTOSIS
## 0.0001000001
## REACTOME_PI3K_EVENTS_IN_ERBB4_SIGNALING
## 0.0001000001
## GAZDA_DIAMOND_BLACKFAN_ANEMIA_MYELOID_UP
## 0.0001000001
## HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_UP
## 0.0002000001
dcor_significant_pathways_p.value <- sort(nominal_dcor_pvalues[nominal_dcor_pvalues <0.05])
length(dcor_significant_pathways_p.value)
## [1] 259
nominal_dcor_q_values <- p.adjust(nominal_dcor_pvalues , method = "fdr")
# nominal_dcor_q_values
nominal_dcor_q_values_under_25 <- sort(nominal_dcor_q_values[nominal_dcor_q_values<0.25])
length((nominal_dcor_q_values_under_25))
## [1] 102
nominal_dcor_q_values_under_25
## REACTOME_GAB1_SIGNALOSOME
## 5.605000e-08
## REACTOME_PI_3K_CASCADE
## 5.605000e-08
## REACTOME_PIP3_ACTIVATES_AKT_SIGNALING
## 5.605000e-08
## GHANDHI_DIRECT_IRRADIATION_UP
## 5.605000e-08
## QUINTENS_EMBRYONIC_BRAIN_RESPONSE_TO_IR
## 5.605000e-08
## MACAEVA_PBMC_RESPONSE_TO_IR
## 5.605000e-08
## KEGG_APOPTOSIS
## 3.736670e-02
## REACTOME_PI3K_EVENTS_IN_ERBB4_SIGNALING
## 3.736670e-02
## GAZDA_DIAMOND_BLACKFAN_ANEMIA_MYELOID_UP
## 3.736670e-02
## HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_UP
## 6.726003e-02
## REACTOME_PI3K_EVENTS_IN_ERBB2_SIGNALING
## 7.760772e-02
## GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP
## 7.760772e-02
## SMIRNOV_RESPONSE_TO_IR_2HR_UP
## 7.760772e-02
## BIOCARTA_ATM_PATHWAY
## 8.407502e-02
## BIOCARTA_KERATINOCYTE_PATHWAY
## 8.407502e-02
## PID_FAS_PATHWAY
## 8.407502e-02
## GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_UP
## 8.407502e-02
## TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP
## 8.407502e-02
## PROVENZANI_METASTASIS_UP
## 8.407502e-02
## MARZEC_IL2_SIGNALING_DN
## 8.407502e-02
## STEIN_ESRRA_TARGETS
## 9.608573e-02
## MOOTHA_PGC
## 1.023522e-01
## WARTERS_IR_RESPONSE_5GY
## 1.023522e-01
## MATZUK_SPERMATOGONIA
## 1.034769e-01
## WARTERS_RESPONSE_TO_IR_SKIN
## 1.034769e-01
## NABA_SECRETED_FACTORS
## 1.034769e-01
## VERHAAK_AML_WITH_NPM1_MUTATED_UP
## 1.080964e-01
## BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN
## 1.080964e-01
## FISCHER_DIRECT_P53_TARGETS_META_ANALYSIS
## 1.275621e-01
## CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5
## 1.345200e-01
## PID_P73PATHWAY
## 1.518774e-01
## MEISSNER_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3
## 1.528636e-01
## DURAND_STROMA_NS_UP
## 1.528636e-01
## KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION
## 1.545162e-01
## BIOCARTA_FAS_PATHWAY
## 1.545162e-01
## BARRIER_CANCER_RELAPSE_NORMAL_SAMPLE_UP
## 1.545162e-01
## MARKS_HDAC_TARGETS_UP
## 1.545162e-01
## WANG_CLIM2_TARGETS_DN
## 1.681500e-01
## AMIT_EGF_RESPONSE_120_MCF10A
## 1.681500e-01
## KANNAN_TP53_TARGETS_UP
## 1.681500e-01
## GENTILE_UV_LOW_DOSE_UP
## 1.681500e-01
## STEIN_ESRRA_TARGETS_UP
## 1.681500e-01
## HELLER_SILENCED_BY_METHYLATION_DN
## 1.720605e-01
## BIOCARTA_MITOCHONDRIA_PATHWAY
## 1.757932e-01
## SESTO_RESPONSE_TO_UV_C0
## 1.793600e-01
## MAGRANGEAS_MULTIPLE_MYELOMA_IGLL_VS_IGLK_UP
## 1.900826e-01
## PID_HIV_NEF_PATHWAY
## 2.004865e-01
## LIU_PROSTATE_CANCER_UP
## 2.004865e-01
## SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_DN
## 2.004865e-01
## MANN_RESPONSE_TO_AMIFOSTINE_UP
## 2.004865e-01
## TSAI_RESPONSE_TO_IONIZING_RADIATION
## 2.004865e-01
## VILIMAS_NOTCH1_TARGETS_DN
## 2.004865e-01
## CORRE_MULTIPLE_MYELOMA_UP
## 2.030491e-01
## SA_CASPASE_CASCADE
## 2.065000e-01
## HAMAI_APOPTOSIS_VIA_TRAIL_DN
## 2.065000e-01
## WU_HBX_TARGETS_2_UP
## 2.065000e-01
## SAGIV_CD24_TARGETS_DN
## 2.065000e-01
## DUTTA_APOPTOSIS_VIA_NFKB
## 2.087379e-01
## BIOCARTA_CERAMIDE_PATHWAY
## 2.109000e-01
## SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_UP
## 2.148583e-01
## GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_UP
## 2.148583e-01
## GOZGIT_ESR1_TARGETS_DN
## 2.148583e-01
## KERLEY_RESPONSE_TO_CISPLATIN_UP
## 2.148583e-01
## KAN_RESPONSE_TO_ARSENIC_TRIOXIDE
## 2.148583e-01
## MAHADEVAN_RESPONSE_TO_MP470_DN
## 2.148583e-01
## WANG_METHYLATED_IN_BREAST_CANCER
## 2.148583e-01
## NAKAJIMA_MAST_CELL
## 2.148583e-01
## LIAN_LIPA_TARGETS_6M
## 2.148583e-01
## LIAN_LIPA_TARGETS_3M
## 2.148583e-01
## COATES_MACROPHAGE_M1_VS_M2_DN
## 2.148583e-01
## MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_UP
## 2.148583e-01
## SMIRNOV_RESPONSE_TO_IR_6HR_UP
## 2.148583e-01
## SATO_SILENCED_BY_DEACETYLATION_IN_PANCREATIC_CANCER
## 2.257356e-01
## KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS
## 2.317743e-01
## KYNG_RESPONSE_TO_H2O2
## 2.331680e-01
## JI_METASTASIS_REPRESSED_BY_STK11
## 2.389500e-01
## MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP
## 2.445818e-01
## KIM_WT1_TARGETS_12HR_UP
## 2.453012e-01
## WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_UP
## 2.453012e-01
## CHUANG_OXIDATIVE_STRESS_RESPONSE_UP
## 2.453012e-01
## VALK_AML_CLUSTER_7
## 2.453012e-01
## POOLA_INVASIVE_BREAST_CANCER_UP
## 2.453012e-01
## WHITFIELD_CELL_CYCLE_M_G1
## 2.453012e-01
## HOELZEL_NF1_TARGETS_UP
## 2.453012e-01
## WANG_TNF_TARGETS
## 2.453012e-01
## REACTOME_FORMATION_OF_INCISION_COMPLEX_IN_GG_NER
## 2.461577e-01
## TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_MONOCYTE_UP
## 2.461577e-01
## LENAOUR_DENDRITIC_CELL_MATURATION_UP
## 2.461577e-01
## CHIARETTI_ACUTE_LYMPHOBLASTIC_LEUKEMIA_ZAP70
## 2.461577e-01
## WANG_SMARCE1_TARGETS_DN
## 2.461577e-01
## WALLACE_PROSTATE_CANCER_UP
## 2.461577e-01
## RUIZ_TNC_TARGETS_UP
## 2.461577e-01
## MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3
## 2.461577e-01
## KASLER_HDAC7_TARGETS_1_UP
## 2.461577e-01
## PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP
## 2.461577e-01
## KATSANOU_ELAVL1_TARGETS_UP
## 2.461577e-01
## KRIEG_HYPOXIA_VIA_KDM3A
## 2.461577e-01
## PID_TAP63_PATHWAY
## 2.472794e-01
## APPIERTO_RESPONSE_TO_FENRETINIDE_UP
## 2.472794e-01
## MOHANKUMAR_HOXA1_TARGETS_DN
## 2.472794e-01
## AMIT_EGF_RESPONSE_120_HELA
## 2.472794e-01
## WU_HBX_TARGETS_1_UP
## 2.472794e-01
nrow(gsea_results_significant)
## [1] 164
length(rownames(gsea_results_significant[gsea_results_significant$FDR.q.val<0.25,]))
## [1] 10
Mutually_identified_in_GSEA_dcor <- intersect(names(dcor_significant_pathways_p.value), rownames(gsea_results_significant))
Mutually_identified_in_GSEA_dcor
## [1] "REACTOME_GAB1_SIGNALOSOME"
## [2] "REACTOME_PIP3_ACTIVATES_AKT_SIGNALING"
## [3] "QUINTENS_EMBRYONIC_BRAIN_RESPONSE_TO_IR"
## [4] "MACAEVA_PBMC_RESPONSE_TO_IR"
## [5] "SMIRNOV_RESPONSE_TO_IR_2HR_UP"
## [6] "WARTERS_IR_RESPONSE_5GY"
## [7] "MATZUK_SPERMATOGONIA"
## [8] "WARTERS_RESPONSE_TO_IR_SKIN"
## [9] "NABA_SECRETED_FACTORS"
## [10] "FISCHER_DIRECT_P53_TARGETS_META_ANALYSIS"
## [11] "PID_P73PATHWAY"
## [12] "KANNAN_TP53_TARGETS_UP"
## [13] "GENTILE_UV_LOW_DOSE_UP"
## [14] "MANN_RESPONSE_TO_AMIFOSTINE_UP"
## [15] "VILIMAS_NOTCH1_TARGETS_DN"
## [16] "LIAN_LIPA_TARGETS_6M"
## [17] "SMIRNOV_RESPONSE_TO_IR_6HR_UP"
## [18] "KERLEY_RESPONSE_TO_CISPLATIN_UP"
## [19] "LIAN_LIPA_TARGETS_3M"
## [20] "PID_TAP63_PATHWAY"
## [21] "RAMALHO_STEMNESS_DN"
## [22] "MCLACHLAN_DENTAL_CARIES_UP"
## [23] "PID_P53_DOWNSTREAM_PATHWAY"
## [24] "BIOCARTA_CHEMICAL_PATHWAY"
## [25] "LABBE_TGFB1_TARGETS_DN"
## [26] "ABE_VEGFA_TARGETS_2HR"
## [27] "BIOCARTA_CK1_PATHWAY"
## [28] "CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP"
## [29] "FOSTER_KDM1A_TARGETS_UP"
## [30] "SU_PANCREAS"
## [31] "REACTOME_AMINE_LIGAND_BINDING_RECEPTORS"
## [32] "MCMURRAY_TP53_HRAS_COOPERATION_RESPONSE_DN"
## [33] "HASLINGER_B_CLL_WITH_CHROMOSOME_12_TRISOMY"
## [34] "ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP"
## [35] "EBAUER_TARGETS_OF_PAX3_FOXO1_FUSION_DN"
Mutually_identified_in_GSEA_dcor_fdr <- intersect(names(nominal_dcor_q_values_under_25),rownames(gsea_results_significant[gsea_results_significant$FDR.q.val<0.25,]))
length(Mutually_identified_in_GSEA_dcor_fdr)
## [1] 5
Significant_in_dcor_not_in_GSEA <- setdiff(names(dcor_significant_pathways_p.value),Mutually_identified_in_GSEA_dcor)
pvalue_of_disparities <- rbind(dcor_significant_pathways_p.value[Significant_in_dcor_not_in_GSEA],gsea_results[Significant_in_dcor_not_in_GSEA,]$NOM.p.val)
rownames(pvalue_of_disparities) <- c("MPEA","GSEA")
pvalue_of_disparities%>%
kable("html", digits = 4, longtable = TRUE) %>%
kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
row_spec(0, angle = -0)
| REACTOME_PI_3K_CASCADE | GHANDHI_DIRECT_IRRADIATION_UP | KEGG_APOPTOSIS | REACTOME_PI3K_EVENTS_IN_ERBB4_SIGNALING | GAZDA_DIAMOND_BLACKFAN_ANEMIA_MYELOID_UP | HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_UP | REACTOME_PI3K_EVENTS_IN_ERBB2_SIGNALING | GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP | BIOCARTA_KERATINOCYTE_PATHWAY | MARZEC_IL2_SIGNALING_DN | BIOCARTA_ATM_PATHWAY | PID_FAS_PATHWAY | GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_UP | TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP | PROVENZANI_METASTASIS_UP | STEIN_ESRRA_TARGETS | MOOTHA_PGC | VERHAAK_AML_WITH_NPM1_MUTATED_UP | BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN | CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5 | MEISSNER_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3 | DURAND_STROMA_NS_UP | KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION | BIOCARTA_FAS_PATHWAY | BARRIER_CANCER_RELAPSE_NORMAL_SAMPLE_UP | MARKS_HDAC_TARGETS_UP | WANG_CLIM2_TARGETS_DN | AMIT_EGF_RESPONSE_120_MCF10A | STEIN_ESRRA_TARGETS_UP | HELLER_SILENCED_BY_METHYLATION_DN | BIOCARTA_MITOCHONDRIA_PATHWAY | SESTO_RESPONSE_TO_UV_C0 | MAGRANGEAS_MULTIPLE_MYELOMA_IGLL_VS_IGLK_UP | SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_DN | LIU_PROSTATE_CANCER_UP | TSAI_RESPONSE_TO_IONIZING_RADIATION | PID_HIV_NEF_PATHWAY | CORRE_MULTIPLE_MYELOMA_UP | SA_CASPASE_CASCADE | HAMAI_APOPTOSIS_VIA_TRAIL_DN | WU_HBX_TARGETS_2_UP | SAGIV_CD24_TARGETS_DN | DUTTA_APOPTOSIS_VIA_NFKB | BIOCARTA_CERAMIDE_PATHWAY | NAKAJIMA_MAST_CELL | WANG_METHYLATED_IN_BREAST_CANCER | GOZGIT_ESR1_TARGETS_DN | KAN_RESPONSE_TO_ARSENIC_TRIOXIDE | SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_UP | GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_UP | MAHADEVAN_RESPONSE_TO_MP470_DN | COATES_MACROPHAGE_M1_VS_M2_DN | MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_UP | SATO_SILENCED_BY_DEACETYLATION_IN_PANCREATIC_CANCER | KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS | KYNG_RESPONSE_TO_H2O2 | JI_METASTASIS_REPRESSED_BY_STK11 | MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP | HOELZEL_NF1_TARGETS_UP | POOLA_INVASIVE_BREAST_CANCER_UP | KIM_WT1_TARGETS_12HR_UP | CHUANG_OXIDATIVE_STRESS_RESPONSE_UP | WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_UP | WHITFIELD_CELL_CYCLE_M_G1 | VALK_AML_CLUSTER_7 | WANG_TNF_TARGETS | WANG_SMARCE1_TARGETS_DN | MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3 | RUIZ_TNC_TARGETS_UP | TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_MONOCYTE_UP | LENAOUR_DENDRITIC_CELL_MATURATION_UP | KATSANOU_ELAVL1_TARGETS_UP | REACTOME_FORMATION_OF_INCISION_COMPLEX_IN_GG_NER | WALLACE_PROSTATE_CANCER_UP | KASLER_HDAC7_TARGETS_1_UP | CHIARETTI_ACUTE_LYMPHOBLASTIC_LEUKEMIA_ZAP70 | PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP | KRIEG_HYPOXIA_VIA_KDM3A | MOHANKUMAR_HOXA1_TARGETS_DN | AMIT_EGF_RESPONSE_120_HELA | WU_HBX_TARGETS_1_UP | APPIERTO_RESPONSE_TO_FENRETINIDE_UP | REACTOME_INTRINSIC_PATHWAY_FOR_APOPTOSIS | KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP | BIOCARTA_BAD_PATHWAY | BOYLAN_MULTIPLE_MYELOMA_C_CLUSTER_UP | MENSSEN_MYC_TARGETS | REACTOME_VOLTAGE_GATED_POTASSIUM_CHANNELS | PRAMOONJAGO_SOX4_TARGETS_UP | SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP | TENEDINI_MEGAKARYOCYTE_MARKERS | BIOCARTA_RAC1_PATHWAY | KANG_IMMORTALIZED_BY_TERT_UP | KIM_MYCN_AMPLIFICATION_TARGETS_UP | PLASARI_TGFB1_SIGNALING_VIA_NFIC_10HR_UP | PACHER_TARGETS_OF_IGF1_AND_IGF2_UP | LIU_SMARCA4_TARGETS | RIGGI_EWING_SARCOMA_PROGENITOR_UP | REACTOME_POTASSIUM_CHANNELS | SHIN_B_CELL_LYMPHOMA_CLUSTER_7 | WINZEN_DEGRADED_VIA_KHSRP | REACTOME_P53_DEPENDENT_G1_DNA_DAMAGE_RESPONSE | BASAKI_YBX1_TARGETS_DN | CONCANNON_APOPTOSIS_BY_EPOXOMICIN_UP | BILD_HRAS_ONCOGENIC_SIGNATURE | OUILLETTE_CLL_13Q14_DELETION_UP | REACTOME_SCFSKP2_MEDIATED_DEGRADATION_OF_P27_P21 | HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_4NM_UP | REACTOME_CYCLIN_E_ASSOCIATED_EVENTS_DURING_G1_S_TRANSITION_ | TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_UP | LAU_APOPTOSIS_CDKN2A_UP | GALLUZZI_PREVENT_MITOCHONDIAL_PERMEABILIZATION | KEGG_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS | SEKI_INFLAMMATORY_RESPONSE_LPS_UP | HOFMANN_MYELODYSPLASTIC_SYNDROM_RISK_UP | REACTOME_CELL_CYCLE_CHECKPOINTS | BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP | REACTOME_SIGNALING_BY_SCF_KIT | REACTOME_ORC1_REMOVAL_FROM_CHROMATIN | HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_DN | ZHANG_PROLIFERATING_VS_QUIESCENT | REACTOME_DOWNSTREAM_SIGNAL_TRANSDUCTION | KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION | REACTOME_SYNTHESIS_OF_DNA | REACTOME_DNA_REPLICATION | BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_UP | BHAT_ESR1_TARGETS_VIA_AKT1_UP | KEGG_PRION_DISEASES | REACTOME_MITOTIC_G2_G2_M_PHASES | NAGASHIMA_NRG1_SIGNALING_UP | PID_CDC42_PATHWAY | GRADE_COLON_AND_RECTAL_CANCER_UP | MIKKELSEN_ES_ICP_WITH_H3K27ME3 | IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_DN | MOOTHA_HUMAN_MITODB_6_2002 | WANG_ESOPHAGUS_CANCER_VS_NORMAL_DN | SEITZ_NEOPLASTIC_TRANSFORMATION_BY_8P_DELETION_DN | DOANE_BREAST_CANCER_ESR1_UP | KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_DN | LEE_NEURAL_CREST_STEM_CELL_DN | GYORFFY_DOXORUBICIN_RESISTANCE | GOLUB_ALL_VS_AML_DN | PID_E2F_PATHWAY | WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_WITH_H4K20ME1_MARK | MORI_SMALL_PRE_BII_LYMPHOCYTE_DN | VALK_AML_CLUSTER_3 | REACTOME_G1_S_TRANSITION | KEGG_INOSITOL_PHOSPHATE_METABOLISM | BIOCARTA_MYOSIN_PATHWAY | BIOCARTA_ACTINY_PATHWAY | REACTOME_CDK_MEDIATED_PHOSPHORYLATION_AND_REMOVAL_OF_CDC6 | REACTOME_REGULATION_OF_MITOTIC_CELL_CYCLE | MULLIGHAN_NPM1_SIGNATURE_3_UP | CHEOK_RESPONSE_TO_MERCAPTOPURINE_DN | MIKKELSEN_ES_ICP_WITH_H3K4ME3 | HOFFMANN_IMMATURE_TO_MATURE_B_LYMPHOCYTE_UP | REACTOME_MITOTIC_M_M_G1_PHASES | BENPORATH_CYCLING_GENES | DARWICHE_SKIN_TUMOR_PROMOTER_DN | VECCHI_GASTRIC_CANCER_EARLY_UP | ELVIDGE_HYPOXIA_BY_DMOG_UP | COATES_MACROPHAGE_M1_VS_M2_UP | NAKAMURA_ADIPOGENESIS_LATE_DN | YAMAZAKI_TCEB3_TARGETS_DN | HOFFMANN_PRE_BI_TO_LARGE_PRE_BII_LYMPHOCYTE_UP | VARELA_ZMPSTE24_TARGETS_UP | REACTOME_G0_AND_EARLY_G1 | HELLER_HDAC_TARGETS_DN | HOEBEKE_LYMPHOID_STEM_CELL_DN | ELVIDGE_HYPOXIA_UP | LANDIS_ERBB2_BREAST_TUMORS_65_UP | ACEVEDO_FGFR1_TARGETS_IN_PROSTATE_CANCER_MODEL_UP | HASLINGER_B_CLL_WITH_MUTATED_VH_GENES | SPIRA_SMOKERS_LUNG_CANCER_UP | BIOCARTA_HIVNEF_PATHWAY | GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_UP | MOOTHA_GLUCONEOGENESIS | MIKKELSEN_IPS_ICP_WITH_H3K27ME3 | PID_RAC1_PATHWAY | PID_RHODOPSIN_PATHWAY | GRADE_COLON_AND_RECTAL_CANCER_DN | SAKAI_TUMOR_INFILTRATING_MONOCYTES_DN | BIOCARTA_CALCINEURIN_PATHWAY | KIM_LIVER_CANCER_POOR_SURVIVAL_DN | PROVENZANI_METASTASIS_DN | SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM6 | SHIN_B_CELL_LYMPHOMA_CLUSTER_8 | PID_BMP_PATHWAY | REACTOME_M_G1_TRANSITION | KRIEG_KDM3A_TARGETS_NOT_HYPOXIA | FERNANDEZ_BOUND_BY_MYC | GALINDO_IMMUNE_RESPONSE_TO_ENTEROTOXIN | REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS | KAUFFMANN_DNA_REPLICATION_GENES | CAFFAREL_RESPONSE_TO_THC_24HR_5_UP | GROSS_HIF1A_TARGETS_DN | LABBE_WNT3A_TARGETS_DN | OHGUCHI_LIVER_HNF4A_TARGETS_UP | VIETOR_IFRD1_TARGETS | LEE_LIVER_CANCER_SURVIVAL_UP | TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINDED_IN_ERYTHROCYTE_UP | GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN | SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_UP | MARCHINI_TRABECTEDIN_RESISTANCE_DN | ROSS_AML_OF_FAB_M7_TYPE | WHITFIELD_CELL_CYCLE_LITERATURE | KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY | REACTOME_PI_METABOLISM | CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_3 | AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_DN | VALK_AML_CLUSTER_16 | WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D | FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_OK_VS_DONOR_DN | ALONSO_METASTASIS_NEURAL_UP | CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_CDC25_DN | KEGG_OOCYTE_MEIOSIS | HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_1_DN | REACTOME_METABOLISM_OF_NUCLEOTIDES | FARMER_BREAST_CANCER_BASAL_VS_LULMINAL | ONDER_CDH1_TARGETS_1_UP | TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_UP | KEGG_NOTCH_SIGNALING_PATHWAY | SMID_BREAST_CANCER_LUMINAL_B_UP | REACTOME_GLUCONEOGENESIS | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MPEA | 0.0000 | 0.0000 | 0.0001 | 0.0001 | 0.0001 | 0.0002 | 0.0003 | 0.0003 | 0.0004 | 0.0004 | 0.0005 | 0.0005 | 0.0005 | 0.0005 | 0.0005 | 0.0006 | 0.0007 | 0.0009 | 0.0009 | 0.0012 | 0.0015 | 0.0015 | 0.0016 | 0.0017 | 0.0017 | 0.0017 | 0.0020 | 0.0020 | 0.0021 | 0.0022 | 0.0023 | 0.0024 | 0.0026 | 0.0029 | 0.0030 | 0.0030 | 0.0031 | 0.0032 | 0.0034 | 0.0035 | 0.0035 | 0.0035 | 0.0036 | 0.0037 | 0.0040 | 0.0041 | 0.0043 | 0.0043 | 0.0045 | 0.0046 | 0.0046 | 0.0046 | 0.0046 | 0.0049 | 0.0051 | 0.0052 | 0.0054 | 0.0056 | 0.0057 | 0.0058 | 0.0059 | 0.0060 | 0.0061 | 0.0061 | 0.0062 | 0.0062 | 0.0063 | 0.0065 | 0.0066 | 0.0067 | 0.0068 | 0.0069 | 0.007 | 0.0070 | 0.0070 | 0.0071 | 0.0071 | 0.0071 | 0.0074 | 0.0074 | 0.0074 | 0.0075 | 0.0078 | 0.0080 | 0.0082 | 0.0082 | 0.0083 | 0.0084 | 0.0084 | 0.0086 | 0.0087 | 0.0088 | 0.0093 | 0.0094 | 0.0094 | 0.0096 | 0.0098 | 0.0098 | 0.0100 | 0.0103 | 0.0106 | 0.0109 | 0.0112 | 0.0115 | 0.0115 | 0.0115 | 0.0116 | 0.0118 | 0.0123 | 0.0123 | 0.0124 | 0.0127 | 0.0131 | 0.0131 | 0.0133 | 0.0139 | 0.0143 | 0.0144 | 0.0145 | 0.0148 | 0.0153 | 0.0163 | 0.0170 | 0.0170 | 0.0176 | 0.0178 | 0.0179 | 0.0182 | 0.0193 | 0.0193 | 0.0197 | 0.0198 | 0.0202 | 0.0206 | 0.0206 | 0.0208 | 0.0208 | 0.0209 | 0.0210 | 0.0216 | 0.0218 | 0.0224 | 0.0232 | 0.0237 | 0.0240 | 0.0241 | 0.0242 | 0.0247 | 0.0248 | 0.0248 | 0.0249 | 0.0251 | 0.0255 | 0.0256 | 0.026 | 0.0261 | 0.0265 | 0.0269 | 0.0271 | 0.0273 | 0.0275 | 0.0275 | 0.0275 | 0.0285 | 0.0289 | 0.0290 | 0.0291 | 0.0293 | 0.0295 | 0.0296 | 0.0302 | 0.0309 | 0.0312 | 0.0318 | 0.0326 | 0.0334 | 0.0336 | 0.0337 | 0.0340 | 0.0341 | 0.0342 | 0.0348 | 0.0349 | 0.0354 | 0.0360 | 0.0362 | 0.0367 | 0.0368 | 0.0371 | 0.0371 | 0.0374 | 0.0375 | 0.0381 | 0.0393 | 0.0403 | 0.0408 | 0.0409 | 0.0410 | 0.0413 | 0.0413 | 0.0420 | 0.0426 | 0.0426 | 0.0426 | 0.0427 | 0.0428 | 0.0432 | 0.0433 | 0.0438 | 0.0440 | 0.0446 | 0.0448 | 0.0454 | 0.0455 | 0.0458 | 0.0466 | 0.0470 | 0.0471 | 0.0485 | 0.0485 | 0.0487 | 0.0490 | 0.0490 | 0.0491 |
| GSEA | 0.2321 | 0.2551 | 0.5364 | 0.1674 | 0.0769 | 0.1869 | 0.2662 | 0.9398 | 0.4801 | 0.9227 | 0.1736 | 0.4680 | 0.0699 | 0.6484 | 0.3756 | 0.4410 | 0.9450 | 0.6571 | 0.1494 | 0.2531 | 0.6642 | 0.1983 | 0.0507 | 0.6530 | 0.6566 | 0.3252 | 0.1663 | 0.5556 | 0.7281 | 0.9698 | 0.3139 | 0.5696 | 0.8706 | 0.5194 | 0.6125 | 0.2661 | 0.4794 | 0.6246 | 0.6592 | 0.0746 | 0.4670 | 0.5405 | 0.0609 | 0.3425 | 0.4614 | 0.5593 | 0.7892 | 0.7223 | 0.2194 | 0.3561 | 0.7326 | 0.3593 | 0.4448 | 0.9314 | 0.5144 | 0.9074 | 0.6964 | 0.5526 | 0.7301 | 0.6568 | 0.9545 | 0.0754 | 0.3996 | 0.5262 | 0.6354 | 0.7523 | 0.4209 | 0.2435 | 0.9976 | 0.9686 | 0.0508 | 0.3245 | 0.474 | 0.7941 | 0.2397 | 0.3301 | 0.3767 | 0.7842 | 0.7064 | 0.5863 | 0.3274 | 0.7107 | 0.0522 | 0.5484 | 0.0635 | 0.4479 | 0.7983 | 0.3642 | 0.4953 | 0.5367 | 0.9282 | 0.3364 | 0.5355 | 0.3342 | 0.8603 | 0.9663 | 0.6195 | 0.9113 | 0.3319 | 0.4894 | 0.8922 | 0.7238 | 0.8142 | 0.9013 | 0.9346 | 0.1835 | 0.7419 | 0.3170 | 0.7361 | 0.6043 | 0.7462 | 0.3943 | 0.3124 | 0.7540 | 0.9412 | 0.4349 | 0.4401 | 0.5251 | 0.6863 | 0.1444 | 0.2260 | 0.1474 | 0.5295 | 0.5717 | 0.4133 | 0.3484 | 0.8831 | 0.2797 | 0.2906 | 0.3210 | 0.9206 | 0.5824 | 0.4437 | 0.5412 | 0.7146 | 0.9611 | 0.0595 | 0.6554 | 0.3117 | 0.5828 | 0.8597 | 0.3410 | 0.5491 | 0.6893 | 0.3177 | 0.6101 | 0.5585 | 0.5199 | 0.6196 | 0.6891 | 0.3209 | 0.2844 | 0.4840 | 0.5017 | 0.500 | 0.2225 | 0.2490 | 0.3605 | 0.0549 | 0.1874 | 0.2559 | 0.5741 | 0.8265 | 0.2085 | 0.0940 | 0.0659 | 0.4388 | 0.3587 | 0.7762 | 0.1821 | 0.0916 | 0.7786 | 0.2547 | 0.3803 | 0.4729 | 0.2368 | 0.6509 | 0.3236 | 0.4141 | 0.3957 | 0.6731 | 0.5282 | 0.1843 | 0.2105 | 0.3824 | 0.6667 | 0.6115 | 0.0833 | 0.3622 | 0.6096 | 0.6126 | 0.4313 | 0.1454 | 0.7944 | 0.3812 | 0.1238 | 0.1708 | 0.8321 | 0.4260 | 0.3101 | 0.4203 | 0.3835 | 0.7438 | 0.9955 | 0.9107 | 0.4195 | 0.2495 | 0.3679 | 0.1652 | 0.7172 | 0.3357 | 0.3618 | 0.0756 | 0.6831 | 0.7266 | 0.3247 | 0.6114 | 0.9388 | 0.2954 | 0.4255 | 0.6801 | 0.3309 | 0.7488 | 0.7050 |
Significant_in_GSEA_not_in_dcor <- setdiff(rownames(gsea_results_significant),Mutually_identified_in_GSEA_dcor)
pvalue_of_disparities <- rbind(nominal_dcor_pvalues[Significant_in_GSEA_not_in_dcor],gsea_results[Significant_in_GSEA_not_in_dcor,]$NOM.p.val)
rownames(pvalue_of_disparities) <- c("MPEA","GSEA")
pvalue_of_disparities %>%
kable("html", digits = 4, longtable = TRUE) %>%
kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
row_spec(0, angle = -0)
| AMUNDSON_DNA_DAMAGE_RESPONSE_TP53 | BIOCARTA_P53_PATHWAY | WILENSKY_RESPONSE_TO_DARAPLADIB | LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN | REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS | BIOCARTA_P53HYPOXIA_PATHWAY | REACTOME_PHASE_II_CONJUGATION | ODONNELL_METASTASIS_UP | REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS | NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON | MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3 | NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_DN | REACTOME_EFFECTS_OF_PIP2_HYDROLYSIS | REACTOME_LIPOPROTEIN_METABOLISM | VALK_AML_CLUSTER_13 | KEGG_P53_SIGNALING_PATHWAY | BIOCARTA_CYTOKINE_PATHWAY | KEGG_CALCIUM_SIGNALING_PATHWAY | VANDESLUIS_COMMD1_TARGETS_GROUP_4_UP | REACTOME_CA_DEPENDENT_EVENTS | CHEN_ETV5_TARGETS_SERTOLI | ONGUSAHA_TP53_TARGETS | TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_DN | REACTOME_REGULATION_OF_IFNA_SIGNALING | BIOCARTA_NO2IL12_PATHWAY | BIOCARTA_INFLAM_PATHWAY | REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES | REACTOME_G_ALPHA_I_SIGNALLING_EVENTS | REACTOME_PLC_BETA_MEDIATED_EVENTS | REACTOME_GPCR_LIGAND_BINDING | REACTOME_DAG_AND_IP3_SIGNALING | CEBALLOS_TARGETS_OF_TP53_AND_MYC_DN | YAUCH_HEDGEHOG_SIGNALING_PARACRINE_DN | PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN | KEGG_OLFACTORY_TRANSDUCTION | MIKKELSEN_MCV6_ICP_WITH_H3K27ME3 | PID_NCADHERIN_PATHWAY | FIGUEROA_AML_METHYLATION_CLUSTER_5_DN | REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS | BREDEMEYER_RAG_SIGNALING_VIA_ATM_NOT_VIA_NFKB_UP | THEODOROU_MAMMARY_TUMORIGENESIS | HOLLEMAN_VINCRISTINE_RESISTANCE_ALL_UP | NIELSEN_SYNOVIAL_SARCOMA_DN | REACTOME_NITRIC_OXIDE_STIMULATES_GUANYLATE_CYCLASE | REACTOME_PHOSPHOLIPASE_C_MEDIATED_CASCADE | MARSON_FOXP3_TARGETS_DN | REACTOME_GPCR_DOWNSTREAM_SIGNALING | GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLACK_UP | REACTOME_LYSOSOME_VESICLE_BIOGENESIS | KAMMINGA_SENESCENCE | ODONNELL_TFRC_TARGETS_UP | GAVIN_FOXP3_TARGETS_CLUSTER_T4 | DARWICHE_PAPILLOMA_PROGRESSION_RISK | YAMASHITA_LIVER_CANCER_STEM_CELL_DN | PEDRIOLI_MIR31_TARGETS_DN | BENPORATH_PRC2_TARGETS | HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN | SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12 | OHGUCHI_LIVER_HNF4A_TARGETS_DN | MA_MYELOID_DIFFERENTIATION_DN | ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_DN | REACTOME_SIGNALING_BY_GPCR | PID_INTEGRIN_CS_PATHWAY | FLORIO_NEOCORTEX_BASAL_RADIAL_GLIA_UP | BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS | XU_HGF_TARGETS_REPRESSED_BY_AKT1_DN | ONO_FOXP3_TARGETS_DN | KEGG_TYPE_I_DIABETES_MELLITUS | HOQUE_METHYLATED_IN_CANCER | ZHANG_GATA6_TARGETS_DN | KONDO_PROSTATE_CANCER_WITH_H3K27ME3 | PID_IL4_2PATHWAY | MIKKELSEN_NPC_HCP_WITH_H3K27ME3 | REN_ALVEOLAR_RHABDOMYOSARCOMA_UP | RIZKI_TUMOR_INVASIVENESS_3D_UP | TAYLOR_METHYLATED_IN_ACUTE_LYMPHOBLASTIC_LEUKEMIA | BROWNE_HCMV_INFECTION_2HR_DN | ANDERSEN_CHOLANGIOCARCINOMA_CLASS2 | REACTOME_ASPARAGINE_N_LINKED_GLYCOSYLATION | MORI_PLASMA_CELL_UP | WANG_RESPONSE_TO_BEXAROTENE_DN | FAELT_B_CLL_WITH_VH3_21_DN | TSENG_ADIPOGENIC_POTENTIAL_UP | KEGG_N_GLYCAN_BIOSYNTHESIS | WELCSH_BRCA1_TARGETS_UP | PID_WNT_NONCANONICAL_PATHWAY | HINATA_NFKB_TARGETS_KERATINOCYTE_DN | REACTOME_GRB2_EVENTS_IN_ERBB2_SIGNALING | BIOCARTA_RAS_PATHWAY | RODRIGUES_NTN1_TARGETS_DN | PID_EPHB_FWD_PATHWAY | BURTON_ADIPOGENESIS_11 | REACTOME_NOTCH1_INTRACELLULAR_DOMAIN_REGULATES_TRANSCRIPTION | REACTOME_PEROXISOMAL_LIPID_METABOLISM | NUYTTEN_NIPP1_TARGETS_DN | BENPORATH_ES_CORE_NINE_CORRELATED | JI_RESPONSE_TO_FSH_DN | DORSAM_HOXA9_TARGETS_UP | PID_HDAC_CLASSI_PATHWAY | BIOCARTA_IGF1_PATHWAY | REACTOME_PROLONGED_ERK_ACTIVATION_EVENTS | PID_HDAC_CLASSII_PATHWAY | AMIT_SERUM_RESPONSE_120_MCF10A | WINTER_HYPOXIA_UP | DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_DN | BARIS_THYROID_CANCER_DN | LANDIS_ERBB2_BREAST_TUMORS_324_UP | SEIDEN_MET_SIGNALING | TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_DN | REACTOME_SHC1_EVENTS_IN_ERBB4_SIGNALING | LEE_AGING_MUSCLE_DN | BIOCARTA_FMLP_PATHWAY | BIOCARTA_NGF_PATHWAY | REACTOME_ENOS_ACTIVATION_AND_REGULATION | GROSS_HYPOXIA_VIA_HIF1A_DN | STONER_ESOPHAGEAL_CARCINOGENESIS_UP | BIOCARTA_BCR_PATHWAY | PID_AVB3_OPN_PATHWAY | SA_B_CELL_RECEPTOR_COMPLEXES | PUIFFE_INVASION_INHIBITED_BY_ASCITES_UP | TRACEY_RESISTANCE_TO_IFNA2_DN | KAAB_FAILED_HEART_ATRIUM_DN | WANG_TUMOR_INVASIVENESS_DN | FORTSCHEGGER_PHF8_TARGETS_DN | SESTO_RESPONSE_TO_UV_C7 | WANG_HCP_PROSTATE_CANCER | REACTOME_CTLA4_INHIBITORY_SIGNALING | KYNG_DNA_DAMAGE_BY_GAMMA_AND_UV_RADIATION | GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MPEA | 0.0518 | 0.1474 | 0.4621 | 0.9999 | 0.1764 | 0.3714 | 0.8323 | 0.9955 | 0.2203 | 0.0862 | 0.4539 | 0.3552 | 0.5429 | 0.2481 | 0.2298 | 0.2731 | 0.9646 | 0.7855 | 0.6565 | 0.1327 | 0.0543 | 0.2684 | 0.2133 | 0.7143 | 0.8424 | 0.6721 | 0.2328 | 0.7396 | 0.2266 | 0.6491 | 0.1319 | 0.5296 | 0.9984 | 0.082 | 0.9686 | 0.6609 | 0.2062 | 0.1085 | 0.2098 | 0.6668 | 0.0885 | 0.3777 | 0.4788 | 0.2443 | 0.1472 | 0.3104 | 0.7955 | 0.1270 | 0.5092 | 0.9549 | 0.5115 | 0.6431 | 0.6050 | 0.9832 | 0.3554 | 0.0606 | 0.6760 | 0.7193 | 0.6484 | 0.4076 | 0.6235 | 0.3036 | 0.6401 | 0.9895 | 0.1885 | 0.5003 | 0.4317 | 0.5914 | 0.7320 | 0.3322 | 0.9974 | 0.7264 | 0.9087 | 0.3551 | 0.4912 | 0.9877 | 0.5798 | 0.6062 | 0.3490 | 0.2290 | 0.4834 | 0.2462 | 0.7869 | 0.1232 | 0.5075 | 0.6393 | 0.6424 | 0.4665 | 0.3850 | 0.9282 | 0.5128 | 0.2434 | 0.4162 | 0.2025 | 0.6619 | 0.6208 | 0.8154 | 0.8192 | 0.7275 | 0.9705 | 0.5150 | 0.7284 | 0.8493 | 0.1807 | 0.9988 | 0.4923 | 0.7746 | 0.9733 | 0.7229 | 0.9456 | 0.2459 | 0.1212 | 0.9899 | 0.3242 | 0.0989 | 0.2780 | 0.3512 | 0.2708 | 0.5926 | 0.0715 | 0.2271 | 0.5188 | 0.1771 | 0.9741 | 0.1885 | 0.5859 | 0.5517 | 0.9505 | 0.2560 |
| GSEA | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.0025 | 0.0044 | 0.0045 | 0.0000 | 0.0070 | 0.0221 | 0.0000 | 0.0022 | 0.0000 | 0.0261 | 0.0217 | 0.0132 | 0.0412 | 0.0025 | 0.0195 | 0.0452 | 0.0217 | 0.0115 | 0.0235 | 0.0345 | 0.0352 | 0.0390 | 0.0141 | 0.0113 | 0.0398 | 0.0246 | 0.0250 | 0.0119 | 0.0118 | 0.026 | 0.0438 | 0.0374 | 0.0041 | 0.0279 | 0.0167 | 0.0392 | 0.0383 | 0.0348 | 0.0466 | 0.0312 | 0.0237 | 0.0321 | 0.0023 | 0.0304 | 0.0317 | 0.0343 | 0.0234 | 0.0350 | 0.0465 | 0.0498 | 0.0363 | 0.0435 | 0.0448 | 0.0260 | 0.0149 | 0.0359 | 0.0499 | 0.0325 | 0.0493 | 0.0209 | 0.0254 | 0.0238 | 0.0477 | 0.0303 | 0.0333 | 0.0406 | 0.0301 | 0.0424 | 0.0464 | 0.0448 | 0.0334 | 0.0000 | 0.0018 | 0.0084 | 0.0172 | 0.0038 | 0.0019 | 0.0134 | 0.0122 | 0.0247 | 0.0018 | 0.0274 | 0.0179 | 0.0164 | 0.0281 | 0.0263 | 0.0232 | 0.0229 | 0.0272 | 0.0234 | 0.0111 | 0.0348 | 0.0469 | 0.0281 | 0.0218 | 0.0216 | 0.0325 | 0.0237 | 0.0423 | 0.0447 | 0.0324 | 0.0144 | 0.0268 | 0.0414 | 0.0318 | 0.0417 | 0.0446 | 0.0323 | 0.0460 | 0.0480 | 0.0364 | 0.0466 | 0.0244 | 0.0456 | 0.0454 | 0.0348 | 0.0479 | 0.0199 | 0.0263 | 0.0275 | 0.0447 | 0.0473 | 0.0422 | 0.0377 | 0.0412 |
# stopCluster(cl)
library(ggfortify)
## Loading required package: ggplot2
for (name in (sort(Significant_in_dcor_not_in_GSEA, decreasing = F))){
strongestpathwaydcor <- unname(unlist(pathway_collapsed[name]))
expressions_pathway <- as.data.frame(expressions[,which(colnames(expressions)%in% strongestpathwaydcor)])
genotypes_category <- ifelse(genotypes==1, "MUT", "WT")
genotypes_category <- as.data.frame(genotypes_category)
print(name)
print(autoplot(prcomp(expressions_pathway), data = genotypes_category, colour='genotypes_category' )+theme_bw())
# pcoa.obj <- pcoa(D = dist(expressions_pathway), correction="none", rn=NULL)
# biplot.pcoa(pcoa.obj)
}
## [1] "ACEVEDO_FGFR1_TARGETS_IN_PROSTATE_CANCER_MODEL_UP"
## [1] "AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_DN"
## [1] "ALONSO_METASTASIS_NEURAL_UP"
## [1] "AMIT_EGF_RESPONSE_120_HELA"
## [1] "AMIT_EGF_RESPONSE_120_MCF10A"
## [1] "APPIERTO_RESPONSE_TO_FENRETINIDE_UP"
## [1] "BARRIER_CANCER_RELAPSE_NORMAL_SAMPLE_UP"
## [1] "BASAKI_YBX1_TARGETS_DN"
## [1] "BENPORATH_CYCLING_GENES"
## [1] "BHAT_ESR1_TARGETS_VIA_AKT1_UP"
## [1] "BILD_HRAS_ONCOGENIC_SIGNATURE"
## [1] "BIOCARTA_ACTINY_PATHWAY"
## [1] "BIOCARTA_ATM_PATHWAY"
## [1] "BIOCARTA_BAD_PATHWAY"
## [1] "BIOCARTA_CALCINEURIN_PATHWAY"
## [1] "BIOCARTA_CERAMIDE_PATHWAY"
## [1] "BIOCARTA_FAS_PATHWAY"
## [1] "BIOCARTA_HIVNEF_PATHWAY"
## [1] "BIOCARTA_KERATINOCYTE_PATHWAY"
## [1] "BIOCARTA_MITOCHONDRIA_PATHWAY"
## [1] "BIOCARTA_MYOSIN_PATHWAY"
## [1] "BIOCARTA_RAC1_PATHWAY"
## [1] "BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP"
## [1] "BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN"
## [1] "BOYLAN_MULTIPLE_MYELOMA_C_CLUSTER_UP"
## [1] "BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_UP"
## [1] "CAFFAREL_RESPONSE_TO_THC_24HR_5_UP"
## [1] "CHEOK_RESPONSE_TO_MERCAPTOPURINE_DN"
## [1] "CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_CDC25_DN"
## [1] "CHIARETTI_ACUTE_LYMPHOBLASTIC_LEUKEMIA_ZAP70"
## [1] "CHUANG_OXIDATIVE_STRESS_RESPONSE_UP"
## [1] "COATES_MACROPHAGE_M1_VS_M2_DN"
## [1] "COATES_MACROPHAGE_M1_VS_M2_UP"
## [1] "CONCANNON_APOPTOSIS_BY_EPOXOMICIN_UP"
## [1] "CORRE_MULTIPLE_MYELOMA_UP"
## [1] "CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_3"
## [1] "CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5"
## [1] "DARWICHE_SKIN_TUMOR_PROMOTER_DN"
## [1] "DOANE_BREAST_CANCER_ESR1_UP"
## [1] "DURAND_STROMA_NS_UP"
## [1] "DUTTA_APOPTOSIS_VIA_NFKB"
## [1] "ELVIDGE_HYPOXIA_BY_DMOG_UP"
## [1] "ELVIDGE_HYPOXIA_UP"
## [1] "FARMER_BREAST_CANCER_BASAL_VS_LULMINAL"
## [1] "FERNANDEZ_BOUND_BY_MYC"
## [1] "FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_OK_VS_DONOR_DN"
## [1] "GALINDO_IMMUNE_RESPONSE_TO_ENTEROTOXIN"
## [1] "GALLUZZI_PREVENT_MITOCHONDIAL_PERMEABILIZATION"
## [1] "GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_UP"
## [1] "GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_UP"
## [1] "GAZDA_DIAMOND_BLACKFAN_ANEMIA_MYELOID_UP"
## [1] "GHANDHI_DIRECT_IRRADIATION_UP"
## [1] "GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_UP"
## [1] "GOLUB_ALL_VS_AML_DN"
## [1] "GOZGIT_ESR1_TARGETS_DN"
## [1] "GRADE_COLON_AND_RECTAL_CANCER_DN"
## [1] "GRADE_COLON_AND_RECTAL_CANCER_UP"
## [1] "GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP"
## [1] "GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN"
## [1] "GROSS_HIF1A_TARGETS_DN"
## [1] "GYORFFY_DOXORUBICIN_RESISTANCE"
## [1] "HAMAI_APOPTOSIS_VIA_TRAIL_DN"
## [1] "HASLINGER_B_CLL_WITH_MUTATED_VH_GENES"
## [1] "HELLER_HDAC_TARGETS_DN"
## [1] "HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_DN"
## [1] "HELLER_SILENCED_BY_METHYLATION_DN"
## [1] "HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_4NM_UP"
## [1] "HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_1_DN"
## [1] "HOEBEKE_LYMPHOID_STEM_CELL_DN"
## [1] "HOELZEL_NF1_TARGETS_UP"
## [1] "HOFFMANN_IMMATURE_TO_MATURE_B_LYMPHOCYTE_UP"
## [1] "HOFFMANN_PRE_BI_TO_LARGE_PRE_BII_LYMPHOCYTE_UP"
## [1] "HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_UP"
## [1] "HOFMANN_MYELODYSPLASTIC_SYNDROM_RISK_UP"
## [1] "IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_DN"
## [1] "JI_METASTASIS_REPRESSED_BY_STK11"
## [1] "KAN_RESPONSE_TO_ARSENIC_TRIOXIDE"
## [1] "KANG_IMMORTALIZED_BY_TERT_UP"
## [1] "KASLER_HDAC7_TARGETS_1_UP"
## [1] "KATSANOU_ELAVL1_TARGETS_UP"
## [1] "KAUFFMANN_DNA_REPLICATION_GENES"
## [1] "KEGG_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS"
## [1] "KEGG_APOPTOSIS"
## [1] "KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION"
## [1] "KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION"
## [1] "KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS"
## [1] "KEGG_INOSITOL_PHOSPHATE_METABOLISM"
## [1] "KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY"
## [1] "KEGG_NOTCH_SIGNALING_PATHWAY"
## [1] "KEGG_OOCYTE_MEIOSIS"
## [1] "KEGG_PRION_DISEASES"
## [1] "KIM_LIVER_CANCER_POOR_SURVIVAL_DN"
## [1] "KIM_MYCN_AMPLIFICATION_TARGETS_UP"
## [1] "KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP"
## [1] "KIM_WT1_TARGETS_12HR_UP"
## [1] "KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_DN"
## [1] "KRIEG_HYPOXIA_VIA_KDM3A"
## [1] "KRIEG_KDM3A_TARGETS_NOT_HYPOXIA"
## [1] "KYNG_RESPONSE_TO_H2O2"
## [1] "LABBE_WNT3A_TARGETS_DN"
## [1] "LANDIS_ERBB2_BREAST_TUMORS_65_UP"
## [1] "LAU_APOPTOSIS_CDKN2A_UP"
## [1] "LEE_LIVER_CANCER_SURVIVAL_UP"
## [1] "LEE_NEURAL_CREST_STEM_CELL_DN"
## [1] "LENAOUR_DENDRITIC_CELL_MATURATION_UP"
## [1] "LIU_PROSTATE_CANCER_UP"
## [1] "LIU_SMARCA4_TARGETS"
## [1] "MAGRANGEAS_MULTIPLE_MYELOMA_IGLL_VS_IGLK_UP"
## [1] "MAHADEVAN_RESPONSE_TO_MP470_DN"
## [1] "MARCHINI_TRABECTEDIN_RESISTANCE_DN"
## [1] "MARKS_HDAC_TARGETS_UP"
## [1] "MARZEC_IL2_SIGNALING_DN"
## [1] "MEISSNER_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3"
## [1] "MENSSEN_MYC_TARGETS"
## [1] "MIKKELSEN_ES_ICP_WITH_H3K27ME3"
## [1] "MIKKELSEN_ES_ICP_WITH_H3K4ME3"
## [1] "MIKKELSEN_IPS_ICP_WITH_H3K27ME3"
## [1] "MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3"
## [1] "MOHANKUMAR_HOXA1_TARGETS_DN"
## [1] "MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_UP"
## [1] "MOOTHA_GLUCONEOGENESIS"
## [1] "MOOTHA_HUMAN_MITODB_6_2002"
## [1] "MOOTHA_PGC"
## [1] "MORI_SMALL_PRE_BII_LYMPHOCYTE_DN"
## [1] "MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP"
## [1] "MULLIGHAN_NPM1_SIGNATURE_3_UP"
## [1] "NAGASHIMA_NRG1_SIGNALING_UP"
## [1] "NAKAJIMA_MAST_CELL"
## [1] "NAKAMURA_ADIPOGENESIS_LATE_DN"
## [1] "OHGUCHI_LIVER_HNF4A_TARGETS_UP"
## [1] "ONDER_CDH1_TARGETS_1_UP"
## [1] "OUILLETTE_CLL_13Q14_DELETION_UP"
## [1] "PACHER_TARGETS_OF_IGF1_AND_IGF2_UP"
## [1] "PID_BMP_PATHWAY"
## [1] "PID_CDC42_PATHWAY"
## [1] "PID_E2F_PATHWAY"
## [1] "PID_FAS_PATHWAY"
## [1] "PID_HIV_NEF_PATHWAY"
## [1] "PID_RAC1_PATHWAY"
## [1] "PID_RHODOPSIN_PATHWAY"
## [1] "PLASARI_TGFB1_SIGNALING_VIA_NFIC_10HR_UP"
## [1] "POOLA_INVASIVE_BREAST_CANCER_UP"
## [1] "PRAMOONJAGO_SOX4_TARGETS_UP"
## [1] "PROVENZANI_METASTASIS_DN"
## [1] "PROVENZANI_METASTASIS_UP"
## [1] "PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP"
## [1] "REACTOME_CDK_MEDIATED_PHOSPHORYLATION_AND_REMOVAL_OF_CDC6"
## [1] "REACTOME_CELL_CYCLE_CHECKPOINTS"
## [1] "REACTOME_CYCLIN_E_ASSOCIATED_EVENTS_DURING_G1_S_TRANSITION_"
## [1] "REACTOME_DNA_REPLICATION"
## [1] "REACTOME_DOWNSTREAM_SIGNAL_TRANSDUCTION"
## [1] "REACTOME_FORMATION_OF_INCISION_COMPLEX_IN_GG_NER"
## [1] "REACTOME_G0_AND_EARLY_G1"
## [1] "REACTOME_G1_S_TRANSITION"
## [1] "REACTOME_GLUCONEOGENESIS"
## [1] "REACTOME_INTRINSIC_PATHWAY_FOR_APOPTOSIS"
## [1] "REACTOME_M_G1_TRANSITION"
## [1] "REACTOME_METABOLISM_OF_NUCLEOTIDES"
## [1] "REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS"
## [1] "REACTOME_MITOTIC_G2_G2_M_PHASES"
## [1] "REACTOME_MITOTIC_M_M_G1_PHASES"
## [1] "REACTOME_ORC1_REMOVAL_FROM_CHROMATIN"
## [1] "REACTOME_P53_DEPENDENT_G1_DNA_DAMAGE_RESPONSE"
## [1] "REACTOME_PI_3K_CASCADE"
## [1] "REACTOME_PI_METABOLISM"
## [1] "REACTOME_PI3K_EVENTS_IN_ERBB2_SIGNALING"
## [1] "REACTOME_PI3K_EVENTS_IN_ERBB4_SIGNALING"
## [1] "REACTOME_POTASSIUM_CHANNELS"
## [1] "REACTOME_REGULATION_OF_MITOTIC_CELL_CYCLE"
## [1] "REACTOME_SCFSKP2_MEDIATED_DEGRADATION_OF_P27_P21"
## [1] "REACTOME_SIGNALING_BY_SCF_KIT"
## [1] "REACTOME_SYNTHESIS_OF_DNA"
## [1] "REACTOME_VOLTAGE_GATED_POTASSIUM_CHANNELS"
## [1] "RIGGI_EWING_SARCOMA_PROGENITOR_UP"
## [1] "ROSS_AML_OF_FAB_M7_TYPE"
## [1] "RUIZ_TNC_TARGETS_UP"
## [1] "SA_CASPASE_CASCADE"
## [1] "SAGIV_CD24_TARGETS_DN"
## [1] "SAKAI_TUMOR_INFILTRATING_MONOCYTES_DN"
## [1] "SATO_SILENCED_BY_DEACETYLATION_IN_PANCREATIC_CANCER"
## [1] "SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_DN"
## [1] "SEITZ_NEOPLASTIC_TRANSFORMATION_BY_8P_DELETION_DN"
## [1] "SEKI_INFLAMMATORY_RESPONSE_LPS_UP"
## [1] "SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_UP"
## [1] "SESTO_RESPONSE_TO_UV_C0"
## [1] "SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM6"
## [1] "SHIN_B_CELL_LYMPHOMA_CLUSTER_7"
## [1] "SHIN_B_CELL_LYMPHOMA_CLUSTER_8"
## [1] "SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_UP"
## [1] "SMID_BREAST_CANCER_LUMINAL_B_UP"
## [1] "SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP"
## [1] "SPIRA_SMOKERS_LUNG_CANCER_UP"
## [1] "STEIN_ESRRA_TARGETS"
## [1] "STEIN_ESRRA_TARGETS_UP"
## [1] "TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_UP"
## [1] "TENEDINI_MEGAKARYOCYTE_MARKERS"
## [1] "TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_UP"
## [1] "TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP"
## [1] "TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINDED_IN_ERYTHROCYTE_UP"
## [1] "TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_MONOCYTE_UP"
## [1] "TSAI_RESPONSE_TO_IONIZING_RADIATION"
## [1] "VALK_AML_CLUSTER_16"
## [1] "VALK_AML_CLUSTER_3"
## [1] "VALK_AML_CLUSTER_7"
## [1] "VARELA_ZMPSTE24_TARGETS_UP"
## [1] "VECCHI_GASTRIC_CANCER_EARLY_UP"
## [1] "VERHAAK_AML_WITH_NPM1_MUTATED_UP"
## [1] "VIETOR_IFRD1_TARGETS"
## [1] "WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D"
## [1] "WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_WITH_H4K20ME1_MARK"
## [1] "WALLACE_PROSTATE_CANCER_UP"
## [1] "WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_UP"
## [1] "WANG_CLIM2_TARGETS_DN"
## [1] "WANG_ESOPHAGUS_CANCER_VS_NORMAL_DN"
## [1] "WANG_METHYLATED_IN_BREAST_CANCER"
## [1] "WANG_SMARCE1_TARGETS_DN"
## [1] "WANG_TNF_TARGETS"
## [1] "WHITFIELD_CELL_CYCLE_LITERATURE"
## [1] "WHITFIELD_CELL_CYCLE_M_G1"
## [1] "WINZEN_DEGRADED_VIA_KHSRP"
## [1] "WU_HBX_TARGETS_1_UP"
## [1] "WU_HBX_TARGETS_2_UP"
## [1] "YAMAZAKI_TCEB3_TARGETS_DN"
## [1] "ZHANG_PROLIFERATING_VS_QUIESCENT"
rownames(gsea_results_significant)
## [1] "AMUNDSON_DNA_DAMAGE_RESPONSE_TP53"
## [2] "WARTERS_IR_RESPONSE_5GY"
## [3] "MANN_RESPONSE_TO_AMIFOSTINE_UP"
## [4] "WARTERS_RESPONSE_TO_IR_SKIN"
## [5] "QUINTENS_EMBRYONIC_BRAIN_RESPONSE_TO_IR"
## [6] "BIOCARTA_P53_PATHWAY"
## [7] "MACAEVA_PBMC_RESPONSE_TO_IR"
## [8] "WILENSKY_RESPONSE_TO_DARAPLADIB"
## [9] "LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN"
## [10] "REACTOME_AMINE_LIGAND_BINDING_RECEPTORS"
## [11] "PID_TAP63_PATHWAY"
## [12] "REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS"
## [13] "BIOCARTA_P53HYPOXIA_PATHWAY"
## [14] "LIAN_LIPA_TARGETS_3M"
## [15] "REACTOME_PHASE_II_CONJUGATION"
## [16] "KERLEY_RESPONSE_TO_CISPLATIN_UP"
## [17] "ODONNELL_METASTASIS_UP"
## [18] "VILIMAS_NOTCH1_TARGETS_DN"
## [19] "REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS"
## [20] "NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON"
## [21] "MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3"
## [22] "PID_P53_DOWNSTREAM_PATHWAY"
## [23] "PID_P73PATHWAY"
## [24] "GENTILE_UV_LOW_DOSE_UP"
## [25] "LIAN_LIPA_TARGETS_6M"
## [26] "NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_DN"
## [27] "REACTOME_EFFECTS_OF_PIP2_HYDROLYSIS"
## [28] "REACTOME_LIPOPROTEIN_METABOLISM"
## [29] "FISCHER_DIRECT_P53_TARGETS_META_ANALYSIS"
## [30] "VALK_AML_CLUSTER_13"
## [31] "KEGG_P53_SIGNALING_PATHWAY"
## [32] "BIOCARTA_CYTOKINE_PATHWAY"
## [33] "BIOCARTA_CK1_PATHWAY"
## [34] "KEGG_CALCIUM_SIGNALING_PATHWAY"
## [35] "VANDESLUIS_COMMD1_TARGETS_GROUP_4_UP"
## [36] "REACTOME_CA_DEPENDENT_EVENTS"
## [37] "ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP"
## [38] "CHEN_ETV5_TARGETS_SERTOLI"
## [39] "ONGUSAHA_TP53_TARGETS"
## [40] "TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_DN"
## [41] "REACTOME_REGULATION_OF_IFNA_SIGNALING"
## [42] "BIOCARTA_NO2IL12_PATHWAY"
## [43] "SU_PANCREAS"
## [44] "BIOCARTA_INFLAM_PATHWAY"
## [45] "REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES"
## [46] "HASLINGER_B_CLL_WITH_CHROMOSOME_12_TRISOMY"
## [47] "REACTOME_G_ALPHA_I_SIGNALLING_EVENTS"
## [48] "REACTOME_PLC_BETA_MEDIATED_EVENTS"
## [49] "MATZUK_SPERMATOGONIA"
## [50] "REACTOME_GPCR_LIGAND_BINDING"
## [51] "REACTOME_DAG_AND_IP3_SIGNALING"
## [52] "CEBALLOS_TARGETS_OF_TP53_AND_MYC_DN"
## [53] "YAUCH_HEDGEHOG_SIGNALING_PARACRINE_DN"
## [54] "PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN"
## [55] "KEGG_OLFACTORY_TRANSDUCTION"
## [56] "MIKKELSEN_MCV6_ICP_WITH_H3K27ME3"
## [57] "KANNAN_TP53_TARGETS_UP"
## [58] "EBAUER_TARGETS_OF_PAX3_FOXO1_FUSION_DN"
## [59] "PID_NCADHERIN_PATHWAY"
## [60] "FIGUEROA_AML_METHYLATION_CLUSTER_5_DN"
## [61] "CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP"
## [62] "REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS"
## [63] "BREDEMEYER_RAG_SIGNALING_VIA_ATM_NOT_VIA_NFKB_UP"
## [64] "THEODOROU_MAMMARY_TUMORIGENESIS"
## [65] "HOLLEMAN_VINCRISTINE_RESISTANCE_ALL_UP"
## [66] "NIELSEN_SYNOVIAL_SARCOMA_DN"
## [67] "MCMURRAY_TP53_HRAS_COOPERATION_RESPONSE_DN"
## [68] "REACTOME_PIP3_ACTIVATES_AKT_SIGNALING"
## [69] "ABE_VEGFA_TARGETS_2HR"
## [70] "REACTOME_NITRIC_OXIDE_STIMULATES_GUANYLATE_CYCLASE"
## [71] "REACTOME_PHOSPHOLIPASE_C_MEDIATED_CASCADE"
## [72] "MARSON_FOXP3_TARGETS_DN"
## [73] "REACTOME_GPCR_DOWNSTREAM_SIGNALING"
## [74] "GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLACK_UP"
## [75] "RAMALHO_STEMNESS_DN"
## [76] "REACTOME_LYSOSOME_VESICLE_BIOGENESIS"
## [77] "FOSTER_KDM1A_TARGETS_UP"
## [78] "KAMMINGA_SENESCENCE"
## [79] "ODONNELL_TFRC_TARGETS_UP"
## [80] "GAVIN_FOXP3_TARGETS_CLUSTER_T4"
## [81] "DARWICHE_PAPILLOMA_PROGRESSION_RISK"
## [82] "YAMASHITA_LIVER_CANCER_STEM_CELL_DN"
## [83] "PEDRIOLI_MIR31_TARGETS_DN"
## [84] "BENPORATH_PRC2_TARGETS"
## [85] "HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN"
## [86] "SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12"
## [87] "SMIRNOV_RESPONSE_TO_IR_2HR_UP"
## [88] "OHGUCHI_LIVER_HNF4A_TARGETS_DN"
## [89] "MA_MYELOID_DIFFERENTIATION_DN"
## [90] "ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_DN"
## [91] "SMIRNOV_RESPONSE_TO_IR_6HR_UP"
## [92] "LABBE_TGFB1_TARGETS_DN"
## [93] "REACTOME_SIGNALING_BY_GPCR"
## [94] "MCLACHLAN_DENTAL_CARIES_UP"
## [95] "BIOCARTA_CHEMICAL_PATHWAY"
## [96] "PID_INTEGRIN_CS_PATHWAY"
## [97] "REACTOME_GAB1_SIGNALOSOME"
## [98] "FLORIO_NEOCORTEX_BASAL_RADIAL_GLIA_UP"
## [99] "NABA_SECRETED_FACTORS"
## [100] "BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS"
## [101] "XU_HGF_TARGETS_REPRESSED_BY_AKT1_DN"
## [102] "ONO_FOXP3_TARGETS_DN"
## [103] "KEGG_TYPE_I_DIABETES_MELLITUS"
## [104] "HOQUE_METHYLATED_IN_CANCER"
## [105] "ZHANG_GATA6_TARGETS_DN"
## [106] "KONDO_PROSTATE_CANCER_WITH_H3K27ME3"
## [107] "PID_IL4_2PATHWAY"
## [108] "MIKKELSEN_NPC_HCP_WITH_H3K27ME3"
## [109] "REN_ALVEOLAR_RHABDOMYOSARCOMA_UP"
## [110] "RIZKI_TUMOR_INVASIVENESS_3D_UP"
## [111] "TAYLOR_METHYLATED_IN_ACUTE_LYMPHOBLASTIC_LEUKEMIA"
## [112] "BROWNE_HCMV_INFECTION_2HR_DN"
## [113] "ANDERSEN_CHOLANGIOCARCINOMA_CLASS2"
## [114] "REACTOME_ASPARAGINE_N_LINKED_GLYCOSYLATION"
## [115] "MORI_PLASMA_CELL_UP"
## [116] "WANG_RESPONSE_TO_BEXAROTENE_DN"
## [117] "FAELT_B_CLL_WITH_VH3_21_DN"
## [118] "TSENG_ADIPOGENIC_POTENTIAL_UP"
## [119] "KEGG_N_GLYCAN_BIOSYNTHESIS"
## [120] "WELCSH_BRCA1_TARGETS_UP"
## [121] "PID_WNT_NONCANONICAL_PATHWAY"
## [122] "HINATA_NFKB_TARGETS_KERATINOCYTE_DN"
## [123] "REACTOME_GRB2_EVENTS_IN_ERBB2_SIGNALING"
## [124] "BIOCARTA_RAS_PATHWAY"
## [125] "RODRIGUES_NTN1_TARGETS_DN"
## [126] "PID_EPHB_FWD_PATHWAY"
## [127] "BURTON_ADIPOGENESIS_11"
## [128] "REACTOME_NOTCH1_INTRACELLULAR_DOMAIN_REGULATES_TRANSCRIPTION"
## [129] "REACTOME_PEROXISOMAL_LIPID_METABOLISM"
## [130] "NUYTTEN_NIPP1_TARGETS_DN"
## [131] "BENPORATH_ES_CORE_NINE_CORRELATED"
## [132] "JI_RESPONSE_TO_FSH_DN"
## [133] "DORSAM_HOXA9_TARGETS_UP"
## [134] "PID_HDAC_CLASSI_PATHWAY"
## [135] "BIOCARTA_IGF1_PATHWAY"
## [136] "REACTOME_PROLONGED_ERK_ACTIVATION_EVENTS"
## [137] "PID_HDAC_CLASSII_PATHWAY"
## [138] "AMIT_SERUM_RESPONSE_120_MCF10A"
## [139] "WINTER_HYPOXIA_UP"
## [140] "DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_DN"
## [141] "BARIS_THYROID_CANCER_DN"
## [142] "LANDIS_ERBB2_BREAST_TUMORS_324_UP"
## [143] "SEIDEN_MET_SIGNALING"
## [144] "TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_DN"
## [145] "REACTOME_SHC1_EVENTS_IN_ERBB4_SIGNALING"
## [146] "LEE_AGING_MUSCLE_DN"
## [147] "BIOCARTA_FMLP_PATHWAY"
## [148] "BIOCARTA_NGF_PATHWAY"
## [149] "REACTOME_ENOS_ACTIVATION_AND_REGULATION"
## [150] "GROSS_HYPOXIA_VIA_HIF1A_DN"
## [151] "STONER_ESOPHAGEAL_CARCINOGENESIS_UP"
## [152] "BIOCARTA_BCR_PATHWAY"
## [153] "PID_AVB3_OPN_PATHWAY"
## [154] "SA_B_CELL_RECEPTOR_COMPLEXES"
## [155] "PUIFFE_INVASION_INHIBITED_BY_ASCITES_UP"
## [156] "TRACEY_RESISTANCE_TO_IFNA2_DN"
## [157] "KAAB_FAILED_HEART_ATRIUM_DN"
## [158] "WANG_TUMOR_INVASIVENESS_DN"
## [159] "FORTSCHEGGER_PHF8_TARGETS_DN"
## [160] "SESTO_RESPONSE_TO_UV_C7"
## [161] "WANG_HCP_PROSTATE_CANCER"
## [162] "REACTOME_CTLA4_INHIBITORY_SIGNALING"
## [163] "KYNG_DNA_DAMAGE_BY_GAMMA_AND_UV_RADIATION"
## [164] "GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN"
for (name in (Significant_in_GSEA_not_in_dcor)){
strongestpathwaydcor <- unname(unlist(pathway_collapsed[name]))
expressions_pathway <- as.data.frame(expressions[,which(colnames(expressions)%in% strongestpathwaydcor)])
genotypes_category <- ifelse(genotypes==1, "MUT", "WT")
genotypes_category <- as.data.frame(genotypes_category)
print(name)
print(autoplot(prcomp(expressions_pathway), data = genotypes_category, colour='genotypes_category' )+theme_bw()+ggtitle(label = "name"))
# pcoa.obj <- pcoa(D = dist(expressions_pathway), correction="none", rn=NULL)
# biplot.pcoa(pcoa.obj)
}
## [1] "AMUNDSON_DNA_DAMAGE_RESPONSE_TP53"
## [1] "BIOCARTA_P53_PATHWAY"
## [1] "WILENSKY_RESPONSE_TO_DARAPLADIB"
## [1] "LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN"
## [1] "REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS"
## [1] "BIOCARTA_P53HYPOXIA_PATHWAY"
## [1] "REACTOME_PHASE_II_CONJUGATION"
## [1] "ODONNELL_METASTASIS_UP"
## [1] "REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS"
## [1] "NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON"
## [1] "MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3"
## [1] "NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_DN"
## [1] "REACTOME_EFFECTS_OF_PIP2_HYDROLYSIS"
## [1] "REACTOME_LIPOPROTEIN_METABOLISM"
## [1] "VALK_AML_CLUSTER_13"
## [1] "KEGG_P53_SIGNALING_PATHWAY"
## [1] "BIOCARTA_CYTOKINE_PATHWAY"
## [1] "KEGG_CALCIUM_SIGNALING_PATHWAY"
## [1] "VANDESLUIS_COMMD1_TARGETS_GROUP_4_UP"
## [1] "REACTOME_CA_DEPENDENT_EVENTS"
## [1] "CHEN_ETV5_TARGETS_SERTOLI"
## [1] "ONGUSAHA_TP53_TARGETS"
## [1] "TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_DN"
## [1] "REACTOME_REGULATION_OF_IFNA_SIGNALING"
## [1] "BIOCARTA_NO2IL12_PATHWAY"
## [1] "BIOCARTA_INFLAM_PATHWAY"
## [1] "REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES"
## [1] "REACTOME_G_ALPHA_I_SIGNALLING_EVENTS"
## [1] "REACTOME_PLC_BETA_MEDIATED_EVENTS"
## [1] "REACTOME_GPCR_LIGAND_BINDING"
## [1] "REACTOME_DAG_AND_IP3_SIGNALING"
## [1] "CEBALLOS_TARGETS_OF_TP53_AND_MYC_DN"
## [1] "YAUCH_HEDGEHOG_SIGNALING_PARACRINE_DN"
## [1] "PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN"
## [1] "KEGG_OLFACTORY_TRANSDUCTION"
## [1] "MIKKELSEN_MCV6_ICP_WITH_H3K27ME3"
## [1] "PID_NCADHERIN_PATHWAY"
## [1] "FIGUEROA_AML_METHYLATION_CLUSTER_5_DN"
## [1] "REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS"
## [1] "BREDEMEYER_RAG_SIGNALING_VIA_ATM_NOT_VIA_NFKB_UP"
## [1] "THEODOROU_MAMMARY_TUMORIGENESIS"
## [1] "HOLLEMAN_VINCRISTINE_RESISTANCE_ALL_UP"
## [1] "NIELSEN_SYNOVIAL_SARCOMA_DN"
## [1] "REACTOME_NITRIC_OXIDE_STIMULATES_GUANYLATE_CYCLASE"
## [1] "REACTOME_PHOSPHOLIPASE_C_MEDIATED_CASCADE"
## [1] "MARSON_FOXP3_TARGETS_DN"
## [1] "REACTOME_GPCR_DOWNSTREAM_SIGNALING"
## [1] "GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLACK_UP"
## [1] "REACTOME_LYSOSOME_VESICLE_BIOGENESIS"
## [1] "KAMMINGA_SENESCENCE"
## [1] "ODONNELL_TFRC_TARGETS_UP"
## [1] "GAVIN_FOXP3_TARGETS_CLUSTER_T4"
## [1] "DARWICHE_PAPILLOMA_PROGRESSION_RISK"
## [1] "YAMASHITA_LIVER_CANCER_STEM_CELL_DN"
## [1] "PEDRIOLI_MIR31_TARGETS_DN"
## [1] "BENPORATH_PRC2_TARGETS"
## [1] "HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN"
## [1] "SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12"
## [1] "OHGUCHI_LIVER_HNF4A_TARGETS_DN"
## [1] "MA_MYELOID_DIFFERENTIATION_DN"
## [1] "ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_DN"
## [1] "REACTOME_SIGNALING_BY_GPCR"
## [1] "PID_INTEGRIN_CS_PATHWAY"
## [1] "FLORIO_NEOCORTEX_BASAL_RADIAL_GLIA_UP"
## [1] "BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS"
## [1] "XU_HGF_TARGETS_REPRESSED_BY_AKT1_DN"
## [1] "ONO_FOXP3_TARGETS_DN"
## [1] "KEGG_TYPE_I_DIABETES_MELLITUS"
## [1] "HOQUE_METHYLATED_IN_CANCER"
## [1] "ZHANG_GATA6_TARGETS_DN"
## [1] "KONDO_PROSTATE_CANCER_WITH_H3K27ME3"
## [1] "PID_IL4_2PATHWAY"
## [1] "MIKKELSEN_NPC_HCP_WITH_H3K27ME3"
## [1] "REN_ALVEOLAR_RHABDOMYOSARCOMA_UP"
## [1] "RIZKI_TUMOR_INVASIVENESS_3D_UP"
## [1] "TAYLOR_METHYLATED_IN_ACUTE_LYMPHOBLASTIC_LEUKEMIA"
## [1] "BROWNE_HCMV_INFECTION_2HR_DN"
## [1] "ANDERSEN_CHOLANGIOCARCINOMA_CLASS2"
## [1] "REACTOME_ASPARAGINE_N_LINKED_GLYCOSYLATION"
## [1] "MORI_PLASMA_CELL_UP"
## [1] "WANG_RESPONSE_TO_BEXAROTENE_DN"
## [1] "FAELT_B_CLL_WITH_VH3_21_DN"
## [1] "TSENG_ADIPOGENIC_POTENTIAL_UP"
## [1] "KEGG_N_GLYCAN_BIOSYNTHESIS"
## [1] "WELCSH_BRCA1_TARGETS_UP"
## [1] "PID_WNT_NONCANONICAL_PATHWAY"
## [1] "HINATA_NFKB_TARGETS_KERATINOCYTE_DN"
## [1] "REACTOME_GRB2_EVENTS_IN_ERBB2_SIGNALING"
## [1] "BIOCARTA_RAS_PATHWAY"
## [1] "RODRIGUES_NTN1_TARGETS_DN"
## [1] "PID_EPHB_FWD_PATHWAY"
## [1] "BURTON_ADIPOGENESIS_11"
## [1] "REACTOME_NOTCH1_INTRACELLULAR_DOMAIN_REGULATES_TRANSCRIPTION"
## [1] "REACTOME_PEROXISOMAL_LIPID_METABOLISM"
## [1] "NUYTTEN_NIPP1_TARGETS_DN"
## [1] "BENPORATH_ES_CORE_NINE_CORRELATED"
## [1] "JI_RESPONSE_TO_FSH_DN"
## [1] "DORSAM_HOXA9_TARGETS_UP"
## [1] "PID_HDAC_CLASSI_PATHWAY"
## [1] "BIOCARTA_IGF1_PATHWAY"
## [1] "REACTOME_PROLONGED_ERK_ACTIVATION_EVENTS"
## [1] "PID_HDAC_CLASSII_PATHWAY"
## [1] "AMIT_SERUM_RESPONSE_120_MCF10A"
## [1] "WINTER_HYPOXIA_UP"
## [1] "DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_DN"
## [1] "BARIS_THYROID_CANCER_DN"
## [1] "LANDIS_ERBB2_BREAST_TUMORS_324_UP"
## [1] "SEIDEN_MET_SIGNALING"
## [1] "TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_DN"
## [1] "REACTOME_SHC1_EVENTS_IN_ERBB4_SIGNALING"
## [1] "LEE_AGING_MUSCLE_DN"
## [1] "BIOCARTA_FMLP_PATHWAY"
## [1] "BIOCARTA_NGF_PATHWAY"
## [1] "REACTOME_ENOS_ACTIVATION_AND_REGULATION"
## [1] "GROSS_HYPOXIA_VIA_HIF1A_DN"
## [1] "STONER_ESOPHAGEAL_CARCINOGENESIS_UP"
## [1] "BIOCARTA_BCR_PATHWAY"
## [1] "PID_AVB3_OPN_PATHWAY"
## [1] "SA_B_CELL_RECEPTOR_COMPLEXES"
## [1] "PUIFFE_INVASION_INHIBITED_BY_ASCITES_UP"
## [1] "TRACEY_RESISTANCE_TO_IFNA2_DN"
## [1] "KAAB_FAILED_HEART_ATRIUM_DN"
## [1] "WANG_TUMOR_INVASIVENESS_DN"
## [1] "FORTSCHEGGER_PHF8_TARGETS_DN"
## [1] "SESTO_RESPONSE_TO_UV_C7"
## [1] "WANG_HCP_PROSTATE_CANCER"
## [1] "REACTOME_CTLA4_INHIBITORY_SIGNALING"
## [1] "KYNG_DNA_DAMAGE_BY_GAMMA_AND_UV_RADIATION"
## [1] "GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN"